Genetic Variant ENSG00000304533:n.240+4149C>T (chr2-102267158-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000804381.1(ENSG00000304533):n.240+4149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,172 control chromosomes in the GnomAD database, including 2,047 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2047 hom., cov: 32)

Consequence

ENSG00000304533
ENST00000804381.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

7 publications found

Variant links:

Genes affected

ENSG00000304533 (HGNC:):

ENSG00000304533 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304533	ENST00000804381.1 link	n.240+4149C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23920

AN:

152054

Hom.:

2048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.150

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.157

AC:

23918

AN:

152172

Hom.:

2047

Cov.:

AF XY:

0.164

AC XY:

12189

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.126

AC:

5248

AN:

41504

American (AMR)

AF:

0.148

AC:

2267

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

385

AN:

3466

East Asian (EAS)

AF:

0.246

AC:

1271

AN:

5164

South Asian (SAS)

AF:

0.324

AC:

1561

AN:

4820

European-Finnish (FIN)

AF:

0.207

AC:

2195

AN:

10596

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.154

AC:

10451

AN:

68004

Other (OTH)

AF:

0.149

AC:

314

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1041

2081

3122

4162

5203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.148

Hom.:

351

Bravo

AF:

0.147

Asia WGS

AF:

0.281

AC:

974

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.21

(source)

DANN

Benign

0.56

PhyloP100

-2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over